popdynMICE: Population dynamics for a MICE model (multiyear)
In Blue-Matter/MSEtool: Management Strategy Evaluation Toolkit

popdynMICE

R Documentation

Population dynamics for a MICE model (multiyear)

Description

Calls popdynOneMICE iteratively to reconstruct a time series given MICE model inputs

Usage

popdynMICE(
  qsx,
  qfracx,
  np,
  nf,
  nyears,
  nareas,
  maxage,
  Nx,
  VFx,
  FretAx,
  Effind,
  movx,
  Spat_targ,
  M_ageArrayx,
  Mat_agex,
  Fec_agex,
  Asizex,
  WatAgex,
  Len_agex,
  Karrayx,
  Linfarrayx,
  t0arrayx,
  Marrayx,
  R0x,
  R0ax,
  SSBpRx,
  hsx,
  aRx,
  bRx,
  ax,
  bx,
  Perrx,
  SRrelx,
  Rel,
  SexPars,
  x,
  plusgroup,
  maxF,
  SSB0x,
  B0x,
  MPA,
  SRRfun,
  SRRpars,
  spawn_time_frac = rep(0, np)
)

Arguments

`qsx`	Total catchability
`qfracx`	Vector `⁠[fleet]⁠`, the fraction of total qs by fleet
`np`	Integer, the number of stocks
`nf`	Integer, number of fleets
`nyears`	Integer, number of historical years (unfished til today)
`nareas`	Integer, the number of spatial areas
`maxage`	Integer, maximum modeled age
`Nx`	Array `⁠[stock, age, year, area]⁠` of stock numbers
`VFx`	Array `⁠[fleet, age, year, area]⁠` of the vulnerability curve
`FretAx`	Array `⁠[fleet, age, year, area]⁠` of the retention curve
`Effind`	Array `⁠[fleet, year]⁠` of effort
`movx`	Array `⁠[stock,age,area,area]⁠` of movement transitions
`Spat_targ`	Matrix `⁠[stock, fleet]⁠` of spatial targeting parameter (0 evenly spatial distributed, 1 proportional to vulnerable biomass)
`M_ageArrayx`	Array `⁠[stock, age,year]⁠` of Natural mortality rate at age
`Mat_agex`	Array `⁠[stock, age, year]⁠` of maturity (spawning fraction) at age
`Fec_agex`	Array `⁠[stock, age, year]⁠` of female spawning weight (fecundity) at age
`Asizex`	Array `⁠[stock, area]⁠` Area size
`WatAgex`	Array of weight-at-age
`Len_agex`	Array of length-at-age
`Karrayx`	Array of von B growth parameter K
`Linfarrayx`	Array of von B asymptotic length parameter Linf
`t0arrayx`	Array ofvon B theoretical age at zero length (t0)
`Marrayx`	Array of mature natural mortality rate
`R0x`	Vector `⁠[stock]⁠` unfished recruitment
`R0ax`	Matrix `⁠[stock, area]⁠` unfished recruitment by area
`SSBpRx`	Matrix `⁠[stock, area]⁠` spawning biomass per recruit by area
`hsx`	Vector `⁠[stock]⁠` steepness of the stock recruitment curve
`aRx`	Vector `⁠[stock]⁠` stock recruitment parameter alpha (for Ricker curve)
`bRx`	Vector `⁠[stock]⁠` stock recruitment parameter beta (for Ricker curve)
`ax`	Vector `⁠[stock]⁠` weight-length parameter a W=aL^b
`bx`	Vector `⁠[stock]⁠` weight-length parameter b W=aL^b
`Perrx`	Matrix `⁠[stock, year]⁠` process error - the lognormal factor for recruitment strength
`SRrelx`	Integer vector `⁠[stock]⁠` the form of the stock recruitment relationship (1 = Beverton-Holt, 2= Ricker)
`Rel`	A list of inter-stock relationships see slot Rel of MOM object class
`SexPars`	A list of sex-specific relationships (SSBfrom, stock_age)
`x`	Integer the simulation number
`plusgroup`	Numeric vector. Use plus-group (1) or not (0)
`maxF`	maximum F
`SSB0x`	SSB0 for this simulation
`B0x`	B0 for this simulation
`MPA`	An array of spatial closures by year `⁠[np,nf,nyears+proyears,nareas]⁠`
`SRRfun`	A list of custom stock-recruit functions. List of length `np`
`SRRpars`	A list of custom stock-recruit parameters for simulation `x`. List of length `np`
`spawn_time_frac`	vector of relative spawn timing. Length nstock